Search publications of the members of the Royal Belgian institute of natural Sciences
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Les structures néandertaliennes de la grotte de Bruniquel : approvisionnement en matériaux et construction - Neanderthal structures in the Bruniquel cave: supply of materials and construction
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Speleothem record from Pentadactylos cave (Cyprus): high-resolution insight into climatic variations during MIS 6 and MIS 5
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Role for researchers in (UNESCO global) geoparks - bibliometric analysis and discussion on national geopark committees
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The Biodiversity of deep-sea Scavenging Amphipoda in the Pacific Ocean. Abstracts of Zoology 2018, Antwerp, Belgium, 13-15.12.18
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The Veldhoven Formation
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The Voort Member
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The Wintelre Member
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The Someren Member
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The Boncelles Formation
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The Poppel Facies
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The Wurfeld Formation
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The Inden Formation
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The Kieseloolite Formation
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The Waubach Member
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The Op-den-Berg Facies
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The Brunssum Member
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The Pey Bed
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The Jagersborg Member
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The Merksplas Formation
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Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing
- Abstract Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
